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- PDB-2nd8: Structures of DK17 in TBLE LUVS -

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Basic information

Entry
Database: PDB / ID: 2nd8
TitleStructures of DK17 in TBLE LUVS
ComponentsCell penetrating peptide
KeywordsLIPID BINDING PROTEIN
Function / homology
Function and homology information


specification of segmental identity, antennal segment / specification of segmental identity, thorax / neuroblast development / muscle cell fate specification / lymph gland development / ventral cord development / anterior/posterior axis specification / anterior/posterior pattern specification / midgut development / regulation of neurogenesis ...specification of segmental identity, antennal segment / specification of segmental identity, thorax / neuroblast development / muscle cell fate specification / lymph gland development / ventral cord development / anterior/posterior axis specification / anterior/posterior pattern specification / midgut development / regulation of neurogenesis / heart development / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleus / cytoplasm
Similarity search - Function
Homeobox protein, antennapedia type / Homeobox protein, antennapedia type, conserved site / 'Homeobox' antennapedia-type protein signature. / Homeobox domain, metazoa / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Homeobox-like domain superfamily
Similarity search - Domain/homology
Homeotic protein antennapedia
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodSOLUTION NMR / distance geometry
Model detailslowest energy, model1
AuthorsBera, S. / Bhunia, A.
CitationJournal: Biochemistry / Year: 2016
Title: Structural Elucidation of the Cell-Penetrating Penetratin Peptide in Model Membranes at the Atomic Level: Probing Hydrophobic Interactions in the Blood-Brain Barrier
Authors: Bera, S. / Kar, R.K. / Mondal, S. / Pahan, K. / Bhunia, A.
History
DepositionMay 11, 2016Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cell penetrating peptide


Theoretical massNumber of molelcules
Total (without water)2,3691
Polymers2,3691
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Cell penetrating peptide


Mass: 2368.869 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Synthetic peptide, modified version of Penetratin peptide, derived from Antennapedia Homeodomain protein (3rd Helix) of Drosophila melanogaster
Source: (synth.) Drosophila melanogaster (fruit fly) / References: UniProt: P02833*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D 1H-1H NOESY

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Sample preparation

DetailsContents: 0.5 mM CELL PENETRATING PEPTIDES-1, 55.5 mM H2O-2, 50 mM D2O-3, 0.5 mM DSS-4, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
0.5 mMCELL PENETRATING PEPTIDES-11
55.5 mMH2O-21
50 mMD2O-31
0.5 mMDSS-41
Sample conditionsIonic strength: 10 / pH: 4.5 / Pressure: ambient / Temperature: 288 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CYANArefinement
RefinementMethod: distance geometry / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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